* FBI genetics expert Claire Fraser-Liggett … I think that the (FBI’s use of the) evidence on science probably was misleading … I have no way to know whether or not Bruce Ivins was really the perpetrator

Posted by Lew Weinstein on October 13, 2011

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Dr. Claire Fraser-Liggett

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Director of the Institute for Genome Sciences, Fraser-Liggett was brought into the investigation to try to trace the DNA found in the anthrax attack letters back to its source material. Based on her team’s research, the FBI zeroed in on a flask controlled by Dr. Bruce Ivins. But while Fraser-Liggett believes the scientific evidence is “very solid,” she is not convinced the government has made its case against Ivins. Below are points extracted from an interview conducted on June 14, 2011.

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The idea behind all of this was that the application of molecular genetics approaches might provide the kind of information that would help to link the material that was sent in the mail back to a source and back to the perpetrator.

the people within the FBI that were put in charge of this investigation were really scrambling to figure out how to put a master plan together that would guide this investigation. …

The pressure was enormous.

we were working in partnership with the FBI but doing a very specific part of this, carrying out a very specific part of this overall investigation. We did not ever know any more than we needed to know to do our job.

We never directly dealt with Bruce Ivins.

If we could find molecular differences that held up and could be traced back to a potential source, that would potentially provide the smoking gun and say, “This is where the material came from.”

LMW: why does no one ever mention the huge stockpile of Ames samples in Iowa that were destroyed immediately after the anthrax attacks in 2001, apparently with the concurrence of the FBI if not its direction?

Once we identified the genetic mutations, we spent a fair amount of time developing assays to target in specifically to those regions that differed.

What they found in looking at these eight samples that contained all four mutations was that they could all be traced back to a single source flask of Bacillus anthracis spores that had been named RMR-1029 and that had been developed and kept at USAMRIID dating back to either 1997 or 1998.

there were perhaps 200 or 300 people at USAMRIID

who had potentially had access to that material

One of the puzzling aspects of the investigation was that there appeared to be two different sources of material … One source that was sent in the letters to New York, to Tom Brokaw and the New York Post, and a second preparation of spores that was sent to Sens. [Tom] Daschle [D-Iowa] and [Patrick] Leahy [D-Vt.].

that suggested that the material that was sent through the mail

didn’t come directly from the 1029 flask

… there had to have been a subsequent preparation step

I think there are still a lot of unanswered questions.

I think there are still a lot of holes,

and I think the FBI is the first to admit that’s the case.

LMW: Not so! The FBI continues to assert that Dr. Ivins was the sole perpetrator

I have no way to know whether or not Bruce Ivins was really the perpetrator.

I think it’s unfortunate in that there were aspects of his personality that made it very easy to cast him as the eccentric, psychologically disturbed scientist with a possible motive. But that doesn’t mean that he’s guilty. …

I absolutely believe that the eight samples that were identified contained the four mutations that were consistent with these samples having been derived from the 1029 flask. It’s consistent with having come from 1029, but that’s different than saying this material absolutely came from 1029.

There probably should have been some more statistical analysis done, looking to see how frequently these kinds of mutations arise when large preparations of Bacillus anthracis are grown up in fermenters.

That was actually an item that was noted in the National Academy’s report. And I can’t say why that work wasn’t done. …

Then there are all sorts of holes in the more traditional aspect of the investigation:

there was no information that ever linked Dr. Ivins to the mailboxes in New Jersey at the times that these letters were presumably sent out;

the fact that it’s known that there were perhaps 200 or more individuals that had access to this material at any point after this flask, this witch’s brew of spores was created. …

the FBI overemphasized the role of science in proving their case.

I think that the (FBI’s use of the) evidence on science

probably was misleading.

The science was very solid, but the science alone could never provide the answers.

There are days when I think there are just still so many unanswered questions that it is absolutely unfair to place guilt on Ivins.

this was not an airtight case, by any means.

no spores were found in (Ivins’) car

think about all the efforts that had to go into decontaminating the postal facilities, and the volatility of these spores, and the fact that they were around for so long, and they went everywhere — to me, that seems like an enormous inconsistency.

I would find it surprising that you could take a piece of equipment in which you had grown any bacterial organism, whether it be anthrax or anything else, and get it completely clean, where there was no trace.

There is absolutely a sense that

there was so much pressure coming from the top,

… that there almost wasn’t time to really think critically

Does that mean that some mistakes were made? Probably, but not with any malicious intent. I don’t think they were ever made with the intent to not get at the truth.

It was always a scramble, and everybody was always reacting to a need for information yesterday rather than tomorrow. Tomorrow was always too late. …

24 Responses to “* FBI genetics expert Claire Fraser-Liggett … I think that the (FBI’s use of the) evidence on science probably was misleading … I have no way to know whether or not Bruce Ivins was really the perpetrator”

DXersaid

As between Steven Salzberg’s spin and Claire Fraser Liggett remarks, I favor Claire Fraser Liggett’s remarks. Although I think both are associated with TIGR, Dr. Salzberg does a disservice to truth with his narrow sound bytes.

DXersaid

Consider Dr. Claire Fraser-Liggett’s observations to this other researcher’s self-congratulatory approach. The author totally overlooks the issue of access to the genetically matching Ames, to include Ames that was thought successfully irradiated but wasn’t.

DXersaid

Amerithrax double-take: Did the FBI finger the wrong person?
submitted by ccondayan on April 14, 2011

Source:www.wired.com

“It had been the most expensive, and arguably the toughest, case in FBI history … but the facts showed that Army biodefense researcher Bruce Ivins was the person responsible for killing five people and sickening 17 others in those frightening weeks after 9/11. It was Ivins, they were now certain, who had mailed the anthrax-filled letters that exposed as many as 30,000 people to the lethal spores.”

“No one involved that day expressed any doubt about Ivins’ guilt. But things are not always as clear-cut as they may seem in an FBI presentation. Two years later, sitting in her office overlooking West Baltimore, Clair Fraser-Liggett, Director, Institute for Genome Sciences, concedes she has reservations. “There are still some holes,” she says, staring out her window in discomfort. Nearly 2,000 miles away in Flagstaff, Arizona, Army biodefense researcher Paul Keim has his own concerns. “I don’t know if Ivins sent the letters,” he says with a hint of both irritation and sadness.”

DXersaid

At the August 18, 2008, the FBI’s genetic consultant explained her background:

“DR. FRASER-LIGGETT: I’m Claire Fraser-Liggett. I’m currently a professor of medicine and director of the Institute for Genome Sciences at the University of Maryland School of Medicine. Prior to last year I was the president and director of the Institute for Genome Sciences that was involved in essentially all of the genome sequencing work related to the Amerithrax investigation. I’ve been involved in the field of comparative microbial genomics since 1995, with the sequencing of the first microbial genome and out of that work have come an interest on my part in using these techniques to better understand microbial evolution and diversity.

At the time of the Anthrax letter mailings in October 2001, we were finishing up the first project to sequence Bacillus Anthracis Ames. It was a strain that was unrelated to the Anthrax letter mailings, but as soon as this news broke, as Dr. Colwell mentioned, we quickly put together a proposal to the National Science Foundation to ask the question as to whether or not genomics-based technologies could be used to identify polymorphisms, that is DNA sequence variance, in different samples of the same isolate of Bacillus Anthracis. The isolate that we were working on for genome analysis also happened to be Bacillus Anthracis Ames as was reported in a paper published in Science in 2002. Indeed, that initial comparative study identified a small number of high-quality snips and we were very encouraged by that initial finding that, indeed, this might be a very useful approach as one part of a large toolbox to be brought to bear on the Amerithrax investigation.

As you’ve also heard in the opening statements, we were then subsequently asked to work with the Bureau to process a large number of samples. This gave us an opportunity to further develop a number of both experimental and computational approaches that had utility not only in the investigation, but I think will also have broader utility of microbial forensics. Many of those approaches were developed by my colleague sitting to my left, Dr. Jacques Ravel.”

DXersaid

DR. FRASER-LIGGETT: That was the comparison of the Porton strain that we had sequenced initially with the Florida strain; and that was just — I think to answer your question, Nick, that was a comparison of one sample that had been collected as part of the investigation and I think what’s been made clear is that in the interest of being thorough what was essential to do was to look at as many different samples as possible that had been collected from the multiple letters in order to get a broader sense of whether the markers that had been identified initially were seen in all samples from the investigation.

QUESTION: In the 2002 paper, there are a large number of markers described. It does include the four markers that were —

DR. FRASER-LIGGETT: Some of them turned out to be found in other samples, but not all of them.

QUESTION: So you —

DR. FRASER-LIGGETT: Correct.

QUESTION: When were the final four markers —

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DR. FRASER-LIGGETT: And I think another important point is that the Florida strain which was related to the Anthrax attacks was a sample that came from the first individual to die of inhalation Anthrax. This was not a sample that came from the spore powders. This was a sample that was obtained from either the blood or the CSFs, I don’t remember, the spinal fluid of the first Anthrax victim. So in that sense, this was a sample, if you will, that was yet one step removed from the powder in the envelope.

The importance of the paper that you’re referring to is the point that Dr. Keim made just a few moments ago; that this was really a proof of principle demonstration that in fact using whole genome sequencing at a sufficient level of coverage, it was possible to identify high-quality polymorphisms. Had we not found any differences whatsoever, that would have put the potential to use these approaches in a whole different light.

DXersaid

In an October 2013 presentation in Croatia, Dr. Keim explained that one challenge faced in Amerithrax was that

“Throughout the investigation, genomic technology was undergoing rapid developments from relying on an 8 locus MLVA system to 15- and 60-locus MLVA systems, to SNP analysis, and finally to WGS — which made trying to validate a system in real time very difficult.” ( p. 32)

DXersaid

Dr. Randall S. Murch, who took the lead in the FBI’s early science investigation in Amerithrax, explained in a June 2014 article:

“Investigators, lawyers, operational and intelligence personnel seek more specific answers to related and included questions, some of which senior leaders and their advisors will also consider: Did a crime or event of interest actually occur? What happened? How did it occur? When did it occur? Where did it occur? Why did it occur? Who was involved or is responsible? What evidence exists, what does it tell us and how strong is it? How reliable and credible is the evidence? What alternative explanations are there for each piece and the sum total of the evidence? Can we defend our conclusions and actions based on the evidence? The answers to all of these questions can be informed, and are often reliant upon, forensic evidence, and in cases in which infectious disease or toxin agents are at issue, microbial forensic evidence. Forensic and specifically microbial forensics can even be used to address more specific aspects of bioterrorism perpetrators and adversaries and their preparation and operational processes, e.g., their concepts and intentions; biological weapons designs, development and dissemination; planning; acquisition, logistics and movement; experimentation; biological agent production and testing; training and preparation; operations and attack; evasion and escape; and, even denial and deception.”

In connection with denial and deception, note that the FBI’s entire reliance of its genetics analysis required that any responsible scientist submit evidence of his guilt. Self-submission was a choice. Maybe it was a necessary choice based on a practical realities. (We can leave that to expert opinion). But it was an important limiting aspect that then was overlooked as a limitation when the zealous prosecutors, eager to declare victory, sought to make a silk purse out of a sow’s ear.

More fundamentally, the FBI spun an analysis that had just narrowed the field from 700 or so to up to 300 or so — and that is just at USAMRIID… as if it pinpointed a particular individual. The FBI then affirmatively misrepresented the evidence at the August 8 press conference — even though the FBI had every reason to know that it had been stored in Building 1412, and not just overnight for aerosol experiments.

DXersaid

In his lucidly written June 2014 article, former senior FBI scientist Randall S. Murch, who had a leading role in Amerithrax early on, wrote:

“Because of the gaps in knowledge with microbial forensics and those fields that are directly leveraged, it certainly can add value in an investigation or operation but both the attributes and limits of what can be derived or provided must be clearly understood, incorporated and communicated so that expectations are managed and decisions are properly constructed. Essential to this is, like other forensic disciplines, microbial forensics has requirements for validation to maximize confidence for performers as stakeholders (Budowle et al. 2008; Schutzer et al. 2009).

A competent microbial forensics capability can add significant benefits and value with, and even be essential to, the investigation and resolution of events involving biological weapons and terrorism; however, because of properties of and gaps in knowledge about the agents themselves and related science, relative newness of the field, the attributes and limitations should be taken into account and used in concert with other sources of information and investigative methods for decision making.”

DXersaid

DXersaid

The US was said to have paid the Thai government $10 million for its role in arresting Sufaat’s boss, Hambali.

Certainly, if Yazid is not interested in coming forward voluntarily with the information about the genetic strain he was using, the information would be worth $5 million paid to Malaysia.

It would be money better spent than the massive amount spent on a genetic analysis narrowing those with access from 700 to “up to 377.” That genetic work was then was trumpeted as if it identified the culprit — when it really merely cut the field by about half (which could have been done by other more routine forensic means).

Indonesia has urged the US to provide access to an Indonesian militant now being held at its Guantanamo Bay camp.
Hambali, the alleged operations chief of South East Asian militant group Jemaah Islamiah, was arrested in Thailand in 2003 and handed to the US.

Since then, Jakarta has had no access to him or news of his whereabouts.

He is one of 14 key terror suspects President Bush confirmed the US was holding when he admitted the existence of secret CIA prisons on Wednesday.

Mr Bush said that the suspects had now been transferred to the detention camp in Cuba and no terror suspects remained in the CIA prisons.

Consular access

Indonesian authorities say they want to speak to Hambali.

“Indonesia has repeatedly asked for the whereabouts of Hambali,” said foreign affairs spokesman Desra Percaya.

“This announcement has given us clarity. We welcome the certainty of his existence.”

On Thursday, officials in the US announced plans to resume military tribunals for Guantanamo detainees, including the 14 suspects.

“Now it is clear where he is, we’re going to request consular access to ensure a fair trial,” Mr Percaya said.

Hambali has been named as a key suspect in a string of bombings across the region.

According to the US, he was the main liaison between Jemaah Islamiah and al-Qaeda from 2000 until his capture in 2003.

Intelligence officials accuse him of planning the first Bali bombing in 2002, in which 202 people died, and raising funds from al-Qaeda for the 2003 attack on the Marriott hotel in Jakarta, which killed 12.

The US was said to have paid $10m to the Thai government for its role in arresting him.

Abstract:
The anthrax letter attacks in October 2001, followed by the SARS outbreak in early 2003, dramatically illustrated our vulnerability to both deliberate and natural outbreaks of infectious disease. The availability of pathogen genome sequences and high-throughput methods for studying the biology of both pathogens and their hosts have provided new insights into the mechanisms of pathogenesis and host defence. As infectious disease research expands to include major bioterror agents, genomics-based approaches will provide one of the cornerstones of efforts to develop more accurate diagnostics, new therapeutics and vaccines, and further capabilities for microbial forensics. INSETS: History of biowarfare and bioterrorism;Comparative genome sequencing: the search for polymorphisms.

The manual for how to respond to an attack should require each researcher to immediately document their time and then for each facility to question its own people immediately. FBI agents can’t do this job.

DXersaid

Nature Medicine 17, 1158–1159 (2011) doi:10.1038/nm1011-1158b
Published online 11 October 2011
A decade ago this month, a microbiologist at Northern Arizona University, in Flagstaff, took a special delivery from the US government. Federal investigators wanted the scientist, Paul Keim, to identify the anthrax that appeared in letters mailed to news organizations and US lawmakers. Overnight, he used PCR to determine that the anthrax sent was the Ames strain, commonly used in research—but that was just the beginning of a scientific investigation that would catapult the still wet-behind-the-ears science of microbial forensics to the forefront of the criminal inquiry.

Ten years on, Keim’s PCR-based technique seems downright quaint in comparison with modern, speedy DNA sequencing. “In a lot of ways we’ve matured,” says Bruce Budowle of the University of North Texas Health Science Center in Fort Worth. But there are challenges ahead, adds Budowle, who retired in 2009 from the US Federal Bureau of Investigation (FBI), where he was involved in the anthrax studies as a senior scientist in the laboratory division: “In a lot of ways, we’ve got a long way to go… We haven’t grown in the interpretation of the results and what they might mean.”